Uncovering novel biological processes and pathogenic mechanisms for glaucoma

揭示青光眼的新生物过程和致病机制

基本信息

批准号：
10413890
负责人：
Ayellet Vered Segre
金额：
$ 74.28万
依托单位：
MASSACHUSETTS EYE AND EAR INFIRMARY
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-06-01 至 2025-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10413890
关键词：
ATAC-seq Affect Alleles Alternative Splicing Autopsy Biological Biological Process Blindness Cell Death Cells Chromatin Ciliary Body Complex Computing Methodologies DNA DNA sequencing Data Disease Disease susceptibility Drug Targeting Etiology Eye Eye diseases Functional disorder Gene Expression Gene Expression Regulation Gene set enrichment analysis Genes Genetic Genetic Transcription Genetic study Genomic Segment Genomics Genotype Genotype-Tissue Expression Project Glaucoma Goals Heritability Human Human Genetics Investigation Lead Link Linkage Disequilibrium Maps Measures Methods Molecular Nerve Degeneration Online Systems Optic Nerve Pathogenicity Pathway interactions Patients Persons Physiologic Intraocular Pressure Predisposition Prevention Primary Open Angle Glaucoma Primary Prevention Protein Isoforms QTL Genes Regulation Research Research Support Resources Retina Retinal Degeneration Retinal Ganglion Cells Risk Risk Factors Statistical Data Interpretation Statistical Methods Structure of sinus venosus of sclera Systems Biology Testing Therapeutic Tissue Sample Tissues Trabecular meshwork structure Translating Untranslated RNA Variant Work causal variant cell type disorder risk functional genomics gene expression variation gene therapy genetic association genetic risk factor genetic variant genome sequencing genome wide association study genomic locus improved insight macula new therapeutic target novel novel therapeutics optic nerve disorder sharing platform single-cell RNA sequencing statistics therapeutic development therapy design trait transcriptome transcriptome sequencing web site whole genome

项目摘要

Project Summary/Abstract Glaucoma is a leading cause of irreversible vision loss affecting 60 million people world-wide. Despite this, prevention and treatment of glaucoma are limited. Primary open angle glaucoma (POAG), the most common form, is characterized by progressive retinal ganglion cell death leading to optic neuropathy, often caused by elevated intraocular pressure (IOP). The long-term goals of the proposed research are to identify genomic regions that affect gene expression in glaucoma-relevant eye tissues, and in combination with large-scale human genetic association studies, to uncover novel causal genes and key biological processes that can lead to glaucoma, which may serve as effective drug targets for novel therapies. Genome-wide association studies (GWAS) have led to the discovery of over 20 genomic loci associated with POAG and over 100 loci associated with IOP, however extracting biological insights from these genetic associations has been challenging, largely due to the fact that the associated variants lie in noncoding regions. Furthermore, much of the heritability of glaucoma has yet to be detected. The Genotype-Tissue Expression (GTEx) project has shown that genetic variants associated with gene expression variation (eQTLs) substantially contribute to disease risk, however GTEx does not contain data for ocular tissues. The working hypothesis of the proposed research, supported by our preliminary results, is that hundreds of regulatory effects will contribute to the pathogenicity of glaucoma and will explain much of its heritability, and that the affected genes will cluster in disease-relevant biological processes. We thus propose in Aim 1, to create a high-quality map of the transcriptome and open chromatin regions (indicative of transcriptional activity), and to identify genetic variants associated with gene expression (eQTLs) and alternative splicing (sQTLs) in four key pathogenic tissues for glaucoma: outflow pathway (trabecular meshwork and Schlemm’s canal), ciliary body, optic nerve, and macular retina, collected from 100 postmortem donors. We will use RNA-seq, ATAC-seq, and whole genome sequencing on bulk tissue and we will further identify cell type-specific eQTLs and sQTLs using cell type-specific gene expression profiles from single cell RNA-seq studies that are available to us. In Aim 2, we will apply novel computational and statistical methods that integrate data from Aim 1 with GWAS data of high or normal-tension glaucoma and several risk factor traits, with the goal of identifying new genetic associations, and the underlying causal genes, pathways, and pathogenic cell types for glaucoma. To broaden the impact of our work, we will build a web-based platform for sharing, browsing, and inspecting gene expression and genetic regulation data from the different eye tissues in relation to genetic associations with glaucoma and other complex eye traits (Aim 3). The proposed research is expected to significantly improve our understanding of the pathophysiology of glaucoma, uncover novel genetic risk factors, and open new avenues for therapeutic development. Our genomics eye resource will also be valuable for studying the molecular causes of other eye diseases, such as retinal degeneration diseases, and for tissue-targeted gene therapy design.

项目摘要/摘要青光眼是不可逆转的视力丧失的主要原因，影响了全球6000万人。尽管如此，青光眼的预防和治疗受到限制。主要的开角青光眼（POAG），最常见的形式，其特征是进行性残留神经节细胞死亡导致视神经病变，通常是由升高引起的眼内压（IOP）。拟议研究的长期目标是确定基因组区域影响与青光眼相关的眼组织中的基因表达，并与大规模的人类通用结合关联研究，以发现可能导致青光眼的新因果基因和关键的生物学过程，这可以作为新型疗法的有效药物靶标。全基因组关联研究（GWAS）已导致发现与POAG相关的20多个基因组基因座和与IOP相关的100多个基因座，但是提取这些遗传关联的生物学见解受到了挑战，这主要是由于相关的事实变体位于非编码区域。此外，青光眼的许多遗传力尚未检测到。这基因型 - 组织表达（GTEX）项目表明，与基因表达相关的遗传变异变异（EQTL）基本上有助于疾病风险，但是GTEX不包含眼组织数据。在我们的初步结果的支持下，拟议研究的工作假设是数百个调节作用将有助于青光眼的致病性，并将解释其遗传力的大部分和受影响的基因将聚集在与疾病相关的生物过程中。因此，我们提出了AIM 1的建议，以创建转录组和开放染色质区域的高质量图（指示转录活性），以及在四个键中识别与基因表达（EQTL）和替代剪接（SQTL）相关的遗传变异青光眼的致病组织：出口通路（小梁网和Schlemm的运河），纤毛体，视神经和黄斑视网膜是从100个验尸供体中收集的。我们将使用RNA-seq，atac-seq和整个基因组测序在散装组织上，我们将进一步鉴定使用细胞类型特异性EQTL和SQTLS 来自单细胞RNA-seq研究的细胞类型特异性基因表达谱。在AIM 2中，我们将应用新颖的计算和统计方法，将目标1与高或高的GWA数据集成到高或正常张力青光眼和几种危险因素特征，目的是确定新的遗传关联，并且青光眼的潜在灾难性基因，途径和致病细胞类型。扩大我们的影响工作，我们将建立一个基于网络的平台，用于共享，浏览和检查基因表达和通用从不同眼组织的调节数据与青光眼和其他复合物的遗传关联有关眼睛特征（AIM 3）。预计拟议的研究将显着提高我们对青光眼的病理生理学，发现新的遗传危险因素和开放治疗的新途径发展。我们的基因组学之眼资源对于研究其他眼睛的分子原因也很有价值疾病，例如残留疾病和针对组织的基因治疗设计。